Evolutionary analyses of myosin genes in trypanosomatids show a history of expansion, secondary losses and neofunctionalization

Figures

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  Figure 1. Schematic of phylogenetic relationships among different trypanosomatids employed in this study based on several works15,42–48. Bodo saltans was represented as outgroup. Coloured boxes represent the presence of different myosin genes. Hashed boxes represent possible gene loss events. Gd – MyoG-derived gene. Hd – MyoH-derived gene. Numbers in circles near some nodes are references to the divergence time estimates in mya (millions years ago), as inferred by Lukes et al.15: 1 – 463-695 mya; 2 – 231-283 mya; 3 – 96-105 mya; 4 – 118-170 mya; 5 – 52-96 mya; 6 – 30-63 mya; 7 – 31-65 mya; 8 – 25-54 mya; 9 – 9-23 mya. The branching is not drawn to scale.

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  Figure 2. Phylogenetic tree of kinetoplastid Class I myosin proteins. The evolutionary history was inferred by using the maximum likelihood method based on the JTT + G (4 categories) model. Bootstrap values from 1,000 replicates are shown next to the branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 34 amino acid sequences. There were 1,185 positions in the final dataset. Phytophthora genus related myosins were used to root the tree. Sequences are identified by the name of species and the GenBank or TritrypDB accession number. Asterisk represents the S. culicis Myo1 sequence obtained from the S. culicis TCC012E genome, contig coordinates AUXH01000328.1:350-4390. T. rangeli sequence (TRSC58_03135) was not included in the phylogeny because it is very short. Protein domain architectures of main sequences are shown.

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  Figure 3. Phylogenetic tree of class XIII myosin proteins. The evolutionary history was inferred using the maximum likelihood method based on the LG + G (4 categories) + I model. Bootstrap values from 1,000 replicates are shown next to the branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 78 amino acid sequences. There were 621 positions of head domain in the final dataset. Saprolegnia parasitica (XP 012197412.1) and Lupinus angustifolius (XP 019460646.1) myosins were used to root the tree. Sequences are identified by the name of species and the GenBank or TritrypDB accession number. Protein domain architectures of main sequences are shown.

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  Figure 4. Phylogenetic tree of kinetoplastid MyoG and MyoG-derived proteins. The evolutionary history was inferred by using the maximum likelihood method based on the JTT + G (4 categories) + I model. Bootstrap values from 1,000 replicates are shown next to the branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 28 amino acid sequences. There were 568 positions in the final dataset. B. saltans MyoG was used to root the tree. Sequences are identified by the name of species and the GenBank or TritrypDB accession number. Protein domain architectures of sequences are shown together with a representation of their genomic context. Due to the high divergence, the A. deanei MyoG-derived protein was not included in the phylogeny.

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  Figure 5. Possible evolutionary scenario of class XIII myosin genes duplications. (A) Representation of 13 putative duplication events (numbered circles) from an ancestral class XIII myosin gene with an unknown primary origin. The order of duplications from 2 to 10 is supported by the phylogeny, while the others are not clear. (B) Possible scenario of evolution where the origin of the first class XIII myosin (yellow star) and duplications 1, 2, 3 and 4 occurred before separation of Kinetoplastida and Herelobosea classes. In this case, some genes were lost in Herelobosea (circles filled with red “X”). (C) Possible scenario of evolution where the origin of the first class XIII myosin (yellow star) and almost all duplication events occurred after separation of the Kinetoplastida and Herelobosea classes. The presence of two copies of this myosin class in Naegleria can be explained by an ancient horizontal transfer event (black arrow) from a kinetoplastid to a Heterolobosea member followed by an event of duplication.